Lecture 16

Question 1

what is a linkage group

Answer 1

all of the genes on a given chromosome are said to be linked or to belong to the same linkage group

Question 2

what is linkage equilibrium?

Answer 2

when loci of different chromosomes hae 50% chance of being packaged together in the same gamete. essentially the equal chance that the diff loci on different chromosomes have to be packaged together

Question 3

what happens to loci on the same chromosome?

Answer 3

because of meiosis and genetic recombination, alleles sometimes get moves from one copy of a chromosome to another

Question 4

what does the probability of loci being swapped by recombination depend on?

Answer 4

depends on the distance between them

Question 4

Loci far apart are ________ linked

Answer 4

less

Question 5

loci close together are _________ linked

Answer 5

tightly

Question 6

what happens if loci are exact opposite ends of the chromosome?

Answer 6

• the loci will often recombine
• all gamete types are equally likely
• maximum possinle rate of 0.5

Question 7

what happens if the loci are so closely linked?

Answer 7

• recombination never occurs
• the rate is 0
• the minimum possinle value the alleles at the two loci are inherited together

Question 8

what is genetic linkage?

Answer 8

refers to the linkage of multiple locu due to the fact they are transmitted through meiosis together

Question 9

what is linkage disequilibrium (D)?

Answer 9

• refers to the relationship between the alleles at different loci
• this may due to physical genetic linkage but does not necessarily always be this

Question 10

when are two loci said to be in linkage disequilibrium?

Answer 10

• D>0
• when knowing the allele at one locus enables you to predict what the allele at the oher locus likely is

Question 11

what is the maximum linkage?

Answer 11

D=0.25 (or -0.25)

Question 12

what is no linkage?

Answer 12

D=0

Question 13

How do we calculate how different the observed frequency of one genotype is compared to the expected

Answer 13

D=Observed-Expected

D=extent of linkage disequilibrium
Observed= observed frequency
Expected= expected freuqnecy if the individuals of the two loci are segregating loci independently (linkage equilibrium)

Question 14

what does it mean when D=0?

Answer 14

zero means no linkage disequilbrium (fully recombining)

Question 15

what eliminates linkage disequilibrium from a population?

Answer 15

• linkage is broken down by recombination
• crossing over during meiosis breaks up old combinations of alleles and creates new combinations
• this takes MORE than a single generation (the process of breaking up disequilbrium between two loci)

Question 16

What are the causes of linkage disequilibrium?

Answer 16

• physical linkage of locus A and locus B on same chromosome
• natural selection (favoring one combination over another)
• gene flow (population structure- AABB individuals arriving in aabb populations)
• assortive mating (AB and AB mate, and ab and ab mate)

Question 17

how can we use linkage disequilibrium?

Answer 17

• sudying migration or dispersal between populations with different gene frequencies or between species
• reconstructing the history of genes and pop.
• indentifying alleles under selection
• mapping of genes of interest

Question 18

Why would we map genes of underlying traits?

Answer 18

• to study the number of genomic regions that influence a quantitative trait
• the magnitude of their effect
• their location in the genome

Question 19

what is quantitative trait locus (QTL)?

Answer 19

• a region of the genome that is correlated with variation in a phenotypic trait
• the region contains the genes (and other genes linked to it) that contribute to population differences in a phenotype

Question 20

What does QTL use?

Answer 20

uses an experiemental cross to create linkage disequilibrium (because only one generation of recombination), and then uses moleculars markers throughout the genome to find the regions where there is statistical association between the phenotype of interest and molecular markers

Question 21

why is QTL analysis helpful?

Answer 21

since each region of a chromosome contributes genes that may or may not affect the trait of interest, by recombining the chromosomes one can find the regions that contribute to the phenotype

Question 22

can we do QTL analysis in humans?

Answer 22

no, so we use different strategies

Question 23

what is genome wide association studies (GWAS)?

Answer 23

• QTL analysis but for humans
• looks for correlations between the genotypes at genetic markers and phenotypic traits
• use existing linkage disequilibrium to find association (because recombination is slowo to break down combination of alleles)

Question 24

what does genome wide association scan for?

Answer 24

GWAS scan for genetic loci associated with disease risk

Question 25

how can we use GWAS to scan for a trait?

Answer 25

* compare frequencies of alleles (SNPs) at each position of the genome for the groups with or without the trait * at casual loci (and the areas around it that are in linkage disequilibrium) will find more differences between the groups than the rest of the genome * would need to be careful about defining the groups tho!!

Question 26

true or false: linkage disequilibrium can mean that multiple genes evolve together (and this can aid in adaptation)

Answer 26

true